+Open data
-Basic information
Entry | Database: PDB / ID: 2dmr | ||||||
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Title | DITHIONITE REDUCED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS | ||||||
Components | DMSO REDUCTASE | ||||||
Keywords | REDUCTASE / DMSO / MOLYBDOPTERIN / DITHIONITE / MONOXO | ||||||
Function / homology | Function and homology information trimethylamine-N-oxide reductase activity / respiratory dimethylsulfoxide reductase / trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / outer membrane-bounded periplasmic space / electron transfer activity Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE MAPS FROM OXIDISED STRUCTURE (BNL-5270) / Resolution: 2.8 Å | ||||||
Authors | Mcalpine, A.S. / Bailey, S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1997 Title: Molybdenum Active Centre of Dmso Reductase from Rhodobacter Capsulatus: Crystal Structure of the Oxidised Enzyme at 1.82-A Resolution and the Dithionite-Reduced Enzyme at 2.8-A Resolution Authors: Mcalpine, A.S. / Mcewan, A.G. / Shaw, A. / Bailey, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Preliminary Crystallographic Studies of Dimethylsulfoxide Reductase from Rhodobacter Capsulatus Authors: Bailey, S. / Mcalpine, A.S. / Duke, E.M.H. / Benson, N. / Mcewan, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dmr.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmr.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmr_validation.pdf.gz | 937 KB | Display | wwPDB validaton report |
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Full document | 2dmr_full_validation.pdf.gz | 952.3 KB | Display | |
Data in XML | 2dmr_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 2dmr_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmr ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 89524.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / Cellular location: PERIPLASM / Strain: H123 / References: UniProt: Q52675 |
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-Non-polymers , 5 types, 112 molecules
#2: Chemical | #3: Chemical | ChemComp-4MO / | #4: Chemical | ChemComp-O / | #5: Chemical | ChemComp-SO2 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 35.2 % Description: MAIN DIFFERENCES AROUND ACTIVE SITE, PICKED OUT IN DIFFERENCE MAPS | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 Details: 0.1M CITRATE BUFFER, PH 4.8 - 5.2 20 - 3% PEG 4000 20% ETHANOL. CRYSTAL SOAKED IN 0.1M DITHIONITE. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion / PH range low: 5.5 / PH range high: 4.7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→36 Å / Num. obs: 17134 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.63 |
Reflection shell | Resolution: 2.8→2.99 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.6 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 74350 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE MAPS FROM OXIDISED STRUCTURE (BNL-5270) Resolution: 2.8→20 Å / Cross valid method: USE OF SINGLE FREE R SET / σ(F): 0 / Details: ONE SO2 MOLECULE
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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